Contacts of the helix formed by residues 27 - 39 (chain P) in PDB entry 2L7F
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 27 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23P ASN* 5.0 1.0 - - - +
26P PRO* 1.3 74.6 - - - +
28P MET* 1.3 68.7 + - - +
29P SER* 3.0 33.8 + - - -
30P THR* 2.9 18.1 + - - +
31P ARG* 2.9 25.5 + - - +
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Residues in contact with MET 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26P PRO 3.6 17.0 - - - +
27P ASP* 1.3 84.2 + - - +
29P SER* 1.3 55.7 + - - +
31P ARG* 3.6 30.9 + - - +
32P GLU* 3.0 27.0 + - - +
42P GLU* 5.0 6.0 - - - +
46P ARG* 4.2 24.9 + - - +
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Residues in contact with SER 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P ASP* 3.0 13.7 + - - -
28P MET* 1.3 74.0 - - - +
30P THR* 1.3 60.4 + - - +
32P GLU* 3.3 11.4 + - - +
33P GLU* 3.0 37.9 + - - +
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Residues in contact with THR 30 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19P THR* 6.5 0.2 - - + -
23P ASN* 5.3 4.0 - - - +
26P PRO* 3.8 21.8 - - + -
27P ASP* 2.9 22.1 + - - +
29P SER* 1.3 74.1 - - - +
31P ARG* 1.3 58.0 + - - +
33P GLU* 3.3 13.9 + - + +
34P ILE* 3.0 39.2 + - + +
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Residues in contact with ARG 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25P TYR* 3.6 23.1 + - - +
26P PRO* 2.8 41.8 + - + +
27P ASP 2.9 14.4 + - - +
28P MET* 3.7 31.1 - - - +
30P THR* 1.3 74.0 - - - +
32P GLU* 1.3 57.7 + - - +
34P ILE* 3.5 13.3 - - - +
35P ALA* 3.0 28.9 + - - +
42P GLU* 4.8 6.5 - - + +
45P VAL* 3.8 13.8 - - + +
46P ARG* 4.7 26.2 - - - +
49P PHE* 3.8 42.5 - - + +
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Residues in contact with GLU 32 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P MET 3.0 16.8 + - - +
29P SER* 3.6 11.4 + - - +
30P THR 3.3 0.2 - - - -
31P ARG* 1.3 74.2 - - - +
33P GLU* 1.3 59.4 + - + +
35P ALA* 3.3 3.9 + - + +
36P VAL* 3.0 36.8 + - + +
42P GLU* 4.0 33.7 - - + +
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Residues in contact with GLU 33 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P SER* 3.0 24.6 + - - +
30P THR* 3.3 13.5 + - + +
32P GLU* 1.3 74.8 - - + +
34P ILE* 1.3 57.0 + - + +
36P VAL* 3.2 8.8 + - - +
37P TRP* 3.0 62.4 + - + +
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Residues in contact with ILE 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P LEU* 3.7 22.2 - - + -
19P THR* 4.0 31.4 - - + +
26P PRO* 5.8 1.3 - - + -
30P THR* 3.0 26.6 + - + +
31P ARG* 3.5 11.0 - - - +
33P GLU* 1.3 75.0 - - + +
35P ALA* 1.3 53.6 + - - +
37P TRP* 3.8 31.0 - - + +
38P THR* 2.8 41.2 + - + +
45P VAL* 3.6 29.6 - - + -
49P PHE* 4.5 2.5 - - + -
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Residues in contact with ALA 35 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31P ARG 3.0 19.0 + - - +
32P GLU* 3.4 7.0 - - + +
34P ILE* 1.3 73.8 - - - +
36P VAL* 1.3 59.1 + - + +
38P THR* 3.2 7.7 + - - -
39P ASN 2.9 10.4 + - - -
40P LEU 2.8 41.3 + - - +
41P THR 3.7 12.3 - - - -
42P GLU* 3.8 5.8 - - - +
45P VAL* 3.7 19.7 - - + -
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Residues in contact with VAL 36 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P GLU* 3.0 25.9 + - + +
33P GLU* 3.2 10.3 + - - +
35P ALA* 1.3 73.8 - - + +
37P TRP* 1.3 72.2 + - + +
39P ASN* 3.2 23.3 + - - +
40P LEU 4.7 2.7 - - - +
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Residues in contact with TRP 37 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P GLU* 5.9 3.5 - - + +
33P GLU* 3.0 51.3 + - + +
34P ILE* 3.8 30.1 - - + +
35P ALA 3.3 0.4 - - - -
36P VAL* 1.3 86.1 - - + +
38P THR* 1.3 59.8 + - + +
39P ASN* 3.8 8.1 + - - -
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Residues in contact with THR 38 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P GLN* 2.8 48.5 + - - +
15P GLU* 3.8 35.2 - - + -
16P LEU* 4.7 10.9 - - + +
19P THR* 6.0 0.7 - - - +
34P ILE* 2.8 26.1 + - + +
35P ALA* 3.2 12.0 + - - -
37P TRP* 1.3 74.7 - - + +
39P ASN* 1.3 59.1 + - - +
40P LEU* 3.6 20.1 - - - +
45P VAL* 4.5 1.7 - - - +
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Residues in contact with ASN 39 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6P THR* 4.6 12.0 - - - +
12P GLN* 4.1 7.3 + - - +
35P ALA 2.9 5.5 + - - -
36P VAL* 3.2 14.0 + - - +
37P TRP 3.9 9.7 + - - -
38P THR* 1.3 82.3 + - - +
40P LEU* 1.3 60.2 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il